Tensorflow concat/split issue in recurrent network example - python-2.7

Consider the following example code:
import tensorflow as tf
import math
import numpy as np
INPUTS = 10
HIDDEN_1 = 20
BATCH_SIZE = 3
def iterate_state(prev_state_tuple, input):
with tf.name_scope('h1'):
weights = tf.get_variable('W', shape=[INPUTS, HIDDEN_1], initializer=tf.truncated_normal_initializer(stddev=1.0 / math.sqrt(float(INPUTS))))
biases = tf.get_variable('bias', shape=[HIDDEN_1], initializer=tf.constant_initializer(0.0))
matmuladd = tf.matmul(inputs, weights) + biases
print("prev state: ",prev_state_tuple.get_shape())
unpacked_state, unpacked_out = tf.split(0,2,prev_state_tuple)
prev_state = unpacked_state
state = 0.9* prev_state + 0.1*matmuladd
output = tf.nn.relu(state)
print(" state: ", state.get_shape())
print(" output: ", output.get_shape())
concat_result = tf.concat(0,[state, output])
print (" concat return: ", concat_result.get_shape())
return concat_result
def data_iter():
while True:
idxs = np.random.rand(BATCH_SIZE, INPUTS)
yield idxs
with tf.Graph().as_default():
inputs = tf.placeholder(tf.float32, shape=(BATCH_SIZE, INPUTS))
with tf.variable_scope('states'):
initial_state = tf.zeros([HIDDEN_1],
name='initial_state')
initial_out = tf.zeros([HIDDEN_1],
name='initial_out')
concat_tensor = tf.concat(0,[initial_state, initial_out])
print(" init state: ",initial_state.get_shape())
print(" init out: ",initial_out.get_shape())
print(" concat: ",concat_tensor.get_shape())
scanout = tf.scan(iterate_state, inputs, initializer=concat_tensor, name='state_scan')
print ("scanout shape: ", scanout.get_shape())
state, output = tf.split(0,2,scanout, name='split_scan_output')
sess = tf.Session()
# Run the Op to initialize the variables.
sess.run(tf.initialize_all_variables())
iter_ = data_iter()
for i in xrange(0, 2):
print ("iteration: ",i)
input_data = iter_.next()
out,st = sess.run([output,state], feed_dict={ inputs: input_data})
I am trying to concatenate and split the internal state and output tensors together so that it can conform to the tf.scan interface.
However, when running this example, I get this error:
(' init state: ', TensorShape([Dimension(20)]))
(' init out: ', TensorShape([Dimension(20)]))
(' concat: ', TensorShape([Dimension(40)]))
('prev state: ', TensorShape([Dimension(40)]))
(' state: ', TensorShape([Dimension(3), Dimension(20)]))
(' output: ', TensorShape([Dimension(3), Dimension(20)]))
(' concat return: ', TensorShape([Dimension(6), Dimension(20)]))
('scanout shape: ', TensorShape(None))
('iteration: ', 0)
Traceback (most recent call last):
File "cycles_in_graphs_with_scan.py", line 57, in <module>
out,st = sess.run([output,state], feed_dict={ inputs: input_data})
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/client/session.py", line 340, in run
run_metadata_ptr)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/client/session.py", line 564, in _run
feed_dict_string, options, run_metadata)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/client/session.py", line 637, in _do_run
target_list, options, run_metadata)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/client/session.py", line 659, in _do_call
e.code)
tensorflow.python.framework.errors.InvalidArgumentError: Number of ways to split should evenly divide the split dimension, but got split_dim 0 (size = 3) and num_split 2
[[Node: states/split_scan_output = Split[T=DT_FLOAT, num_split=2, _device="/job:localhost/replica:0/task:0/cpu:0"](states/split_scan_output/split_dim, states/state_scan/TensorArrayPack)]]
Caused by op u'states/split_scan_output', defined at:
File "cycles_in_graphs_with_scan.py", line 46, in <module>
state, output = tf.split(0,2,scanout, name='split_scan_output')
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/ops/array_ops.py", line 525, in split
name=name)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/ops/gen_array_ops.py", line 1428, in _split
num_split=num_split, name=name)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/ops/op_def_library.py", line 655, in apply_op
op_def=op_def)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/framework/ops.py", line 2154, in create_op
original_op=self._default_original_op, op_def=op_def)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/framework/ops.py", line 1154, in __init__
self._traceback = _extract_stack()
while the return tensor has clearly dimensions (6,20) as shown, the return from tf.scan seems to have a shape of None, while the error says that it is finding an object of length 3
Any idea what might be causing this error?

It looks like the tf.scan() function is unable to infer a static shape for the output, and thus you're getting a runtime failure when you try to split scanout into 2 tensors on the 0th dimension.
In cases like this, the best thing to do is to evaluate scanout to see what its actual shape is:
sess = tf.Session()
sess.run(tf.initialize_all_variables())
iter_ = data_iter()
input_data = iter_.next()
scanout_val = sess.run(scanout, feed_dict={inputs: input_data})
print("Actual shape of scanout:", scanout_val.shape)
From the error message it looks like it has size 3 in the 0th dimension, which I suspect comes from the batch size, because the 0th dimension of tf.scan()'s input and output will have the same size. One possibility is that you actually want to split on the 1st dimension:
state, output = tf.split(1, 2, scanout, name='split_scan_output')

Related

Tensorflow 1.0 Seq2Seq Decoder function

I'm trying to make a Seq2Seq Regression example for time-series analysis and I've used the Seq2Seq library as presented at the Dev Summit, which is currently the code on the Tensorflow GitHub branch r1.0.
I have difficulties understanding how the decoder function works for Seq2Seq, specifically for the "cell_output".
I understand that the num_decoder_symbols is the number of classes/words to decode at each time step. I have it working at a point where I can do training. However, I don't get why I can't just substitute the number of features (num_features) instead of num_decoder_symbols. Basically, I want to be able to run the decoder without teacher forcing, in other words pass the output of the previous time step as the input to the next time step.
with ops.name_scope(name, "simple_decoder_fn_inference",
[time, cell_state, cell_input, cell_output,
context_state]):
if cell_input is not None:
raise ValueError("Expected cell_input to be None, but saw: %s" %
cell_input)
if cell_output is None:
# invariant that this is time == 0
next_input_id = array_ops.ones([batch_size,], dtype=dtype) * (
start_of_sequence_id)
done = array_ops.zeros([batch_size,], dtype=dtypes.bool)
cell_state = encoder_state
cell_output = array_ops.zeros([num_decoder_symbols],
dtype=dtypes.float32)
Here is a link to the original code: https://github.com/tensorflow/tensorflow/blob/r1.0/tensorflow/contrib/seq2seq/python/ops/decoder_fn.py
Why don't I need to pass batch_size for the cell output?
cell_output = array_ops.zeros([batch_size, num_decoder_symbols],
dtype=dtypes.float32)
When trying to use this code to create my own regressive Seq2Seq example, where instead of having an output of probabilities/classes, I have a real valued vector of dimension num_features, instead of an array of probability of classes. As I understood, I thought I could replace num_decoder_symbols with num_features, like below:
def decoder_fn(time, cell_state, cell_input, cell_output, context_state):
"""
Again same as in simple_decoder_fn_inference but for regression on sequences with a fixed length
"""
with ops.name_scope(name, "simple_decoder_fn_inference", [time, cell_state, cell_input, cell_output, context_state]):
if cell_input is not None:
raise ValueError("Expected cell_input to be None, but saw: %s" % cell_input)
if cell_output is None:
# invariant that this is time == 0
next_input = array_ops.ones([batch_size, num_features], dtype=dtype)
done = array_ops.zeros([batch_size], dtype=dtypes.bool)
cell_state = encoder_state
cell_output = array_ops.zeros([num_features], dtype=dtypes.float32)
else:
cell_output = output_fn(cell_output)
done = math_ops.equal(0,1) # hardcoded hack just to properly define done
next_input = cell_output
# if time > maxlen, return all true vector
done = control_flow_ops.cond(math_ops.greater(time, maximum_length),
lambda: array_ops.ones([batch_size,], dtype=dtypes.bool),
lambda: done)
return (done, cell_state, next_input, cell_output, context_state)
return decoder_fn
But, I get the following error:
File "/opt/DL/tensorflow/lib/python2.7/site-packages/tensorflow/contrib/seq2seq/python/ops/seq2seq.py", line 212, in dynamic_rnn_decoder
swap_memory=swap_memory, scope=scope)
File "/opt/DL/tensorflow/lib/python2.7/site-packages/tensorflow/python/ops/rnn.py", line 1036, in raw_rnn
swap_memory=swap_memory)
File "/opt/DL/tensorflow/lib/python2.7/site-packages/tensorflow/python/ops/control_flow_ops.py", line 2605, in while_loop
result = context.BuildLoop(cond, body, loop_vars, shape_invariants)
File "/opt/DL/tensorflow/lib/python2.7/site-packages/tensorflow/python/ops/control_flow_ops.py", line 2438, in BuildLoop
pred, body, original_loop_vars, loop_vars, shape_invariants)
File "/opt/DL/tensorflow/lib/python2.7/site-packages/tensorflow/python/ops/control_flow_ops.py", line 2388, in _BuildLoop
body_result = body(*packed_vars_for_body)
File "/opt/DL/tensorflow/lib/python2.7/site-packages/tensorflow/python/ops/rnn.py", line 980, in body
(next_output, cell_state) = cell(current_input, state)
File "/opt/DL/tensorflow/lib/python2.7/site-packages/tensorflow/contrib/rnn/python/ops/core_rnn_cell_impl.py", line 327, in __call__
input_size = inputs.get_shape().with_rank(2)[1]
File "/opt/DL/tensorflow/lib/python2.7/site-packages/tensorflow/python/framework/tensor_shape.py", line 635, in with_rank
raise ValueError("Shape %s must have rank %d" % (self, rank))
ValueError: Shape (100,) must have rank 2
As a result, I passed in the batch_size like this in order to get a Shape of rank 2:
cell_output = array_ops.zeros([batch_size, num_features],
dtype=dtypes.float32)
But I get the following error, where Shape is of rank 3 and wants a rank 2 instead:
File "/opt/DL/tensorflow/lib/python2.7/site-packages/tensorflow/contrib/seq2seq/python/ops/seq2seq.py", line 212, in dynamic_rnn_decoder
swap_memory=swap_memory, scope=scope)
File "/opt/DL/tensorflow/lib/python2.7/site-packages/tensorflow/python/ops/rnn.py", line 1036, in raw_rnn
swap_memory=swap_memory)
File "/opt/DL/tensorflow/lib/python2.7/site-packages/tensorflow/python/ops/control_flow_ops.py", line 2605, in while_loop
result = context.BuildLoop(cond, body, loop_vars, shape_invariants)
File "/opt/DL/tensorflow/lib/python2.7/site-packages/tensorflow/python/ops/control_flow_ops.py", line 2438, in BuildLoop
pred, body, original_loop_vars, loop_vars, shape_invariants)
File "/opt/DL/tensorflow/lib/python2.7/site-packages/tensorflow/python/ops/control_flow_ops.py", line 2388, in _BuildLoop
body_result = body(*packed_vars_for_body)
File "/opt/DL/tensorflow/lib/python2.7/site-packages/tensorflow/python/ops/rnn.py", line 980, in body
(next_output, cell_state) = cell(current_input, state)
File "/opt/DL/tensorflow/lib/python2.7/site-packages/tensorflow/contrib/rnn/python/ops/core_rnn_cell_impl.py", line 327, in __call__
input_size = inputs.get_shape().with_rank(2)[1]
File "/opt/DL/tensorflow/lib/python2.7/site-packages/tensorflow/python/framework/tensor_shape.py", line 635, in with_rank
raise ValueError("Shape %s must have rank %d" % (self, rank))
ValueError: Shape (10, 10, 100) must have rank 2

RNN regression using Tensorflow?

I am currently trying to implement a RNN for regression.
I need to create a neural network capable of converting audio samples into vector of mfcc feature. I've already know what the feature for each audio samples is, so the task it self is to create a neural network that is capable of converting a list of audio samples in to the desired MFCC feature.
The second problem I am facing is that since the audio files I am sampling has different length, will the list with the audio sample also have different length, which would cause problem with the number of input I need to feed into to the neural network. I found this post on how to handle variable sequence length, and tried to incorporate into my implementation of a RNN, but seem to not be able to get a lot of errors for unexplainable reasons..
Could anyone see what is going wrong with my implementation?
Here is the code:
def length(sequence): ##Zero padding to fit the max lenght... Question whether that is a good idea.
used = tf.sign(tf.reduce_max(tf.abs(sequence), reduction_indices=2))
length = tf.reduce_sum(used, reduction_indices=1)
length = tf.cast(length, tf.int32)
return length
def cost(output, target):
# Compute cross entropy for each frame.
cross_entropy = target * tf.log(output)
cross_entropy = -tf.reduce_sum(cross_entropy, reduction_indices=2)
mask = tf.sign(tf.reduce_max(tf.abs(target), reduction_indices=2))
cross_entropy *= mask
# Average over actual sequence lengths.
cross_entropy = tf.reduce_sum(cross_entropy, reduction_indices=1)
cross_entropy /= tf.reduce_sum(mask, reduction_indices=1)
return tf.reduce_mean(cross_entropy)
def last_relevant(output):
max_length = int(output.get_shape()[1])
relevant = tf.reduce_sum(tf.mul(output, tf.expand_dims(tf.one_hot(length, max_length), -1)), 1)
return relevant
files_train_path = [dnn_train+f for f in listdir(dnn_train) if isfile(join(dnn_train, f))]
files_test_path = [dnn_test+f for f in listdir(dnn_test) if isfile(join(dnn_test, f))]
files_train_name = [f for f in listdir(dnn_train) if isfile(join(dnn_train, f))]
files_test_name = [f for f in listdir(dnn_test) if isfile(join(dnn_test, f))]
os.chdir(dnn_train)
train_name,train_data = generate_list_of_names_data(files_train_path)
train_data, train_names, train_output_data, train_class_output = load_sound_files(files_train_path,train_name,train_data)
max_length = 0 ## Used for variable sequence input
for element in train_data:
if element.size > max_length:
max_length = element.size
NUM_EXAMPLES = len(train_data)/2
test_data = train_data[NUM_EXAMPLES:]
test_output = train_output_data[NUM_EXAMPLES:]
train_data = train_data[:NUM_EXAMPLES]
train_output = train_output_data[:NUM_EXAMPLES]
print("--- %s seconds ---" % (time.time() - start_time))
#----------------------------------------------------------------------#
#----------------------------Main--------------------------------------#
### Tensorflow neural network setup
batch_size = None
sequence_length_max = max_length
input_dimension=1
data = tf.placeholder(tf.float32,[batch_size,sequence_length_max,input_dimension])
target = tf.placeholder(tf.float32,[None,14])
num_hidden = 24 ## Hidden layer
cell = tf.nn.rnn_cell.LSTMCell(num_hidden,state_is_tuple=True) ## Long short term memory
output, state = tf.nn.dynamic_rnn(cell, data, dtype=tf.float32,sequence_length = length(data)) ## Creates the Rnn skeleton
last = last_relevant(output)#tf.gather(val, int(val.get_shape()[0]) - 1) ## Appedning as last
weight = tf.Variable(tf.truncated_normal([num_hidden, int(target.get_shape()[1])]))
bias = tf.Variable(tf.constant(0.1, shape=[target.get_shape()[1]]))
prediction = tf.nn.softmax(tf.matmul(last, weight) + bias)
cross_entropy = cost(output,target)# How far am I from correct value?
optimizer = tf.train.AdamOptimizer() ## TensorflowOptimizer
minimize = optimizer.minimize(cross_entropy)
mistakes = tf.not_equal(tf.argmax(target, 1), tf.argmax(prediction, 1))
error = tf.reduce_mean(tf.cast(mistakes, tf.float32))
## Training ##
init_op = tf.initialize_all_variables()
sess = tf.Session()
sess.run(init_op)
batch_size = 1000
no_of_batches = int(len(train_data)/batch_size)
epoch = 5000
for i in range(epoch):
ptr = 0
for j in range(no_of_batches):
inp, out = train_data[ptr:ptr+batch_size], train_output[ptr:ptr+batch_size]
ptr+=batch_size
sess.run(minimize,{data: inp, target: out})
print "Epoch - ",str(i)
incorrect = sess.run(error,{data: test_data, target: test_output})
print('Epoch {:2d} error {:3.1f}%'.format(i + 1, 100 * incorrect))
sess.close()
Error message:
Traceback (most recent call last):
File "tensorflow_test.py", line 177, in <module>
last = last_relevant(output)#tf.gather(val, int(val.get_shape()[0]) - 1) ## Appedning as last
File "tensorflow_test.py", line 132, in last_relevant
relevant = tf.reduce_sum(tf.mul(output, tf.expand_dims(tf.one_hot(length, max_length), -1)), 1)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/ops/array_ops.py", line 2778, in one_hot
name)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/ops/gen_array_ops.py", line 1413, in _one_hot
axis=axis, name=name)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/framework/op_def_library.py", line 454, in apply_op
as_ref=input_arg.is_ref)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/framework/ops.py", line 621, in convert_to_tensor
ret = conversion_func(value, dtype=dtype, name=name, as_ref=as_ref)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/framework/constant_op.py", line 180, in _constant_tensor_conversion_function
return constant(v, dtype=dtype, name=name)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/framework/constant_op.py", line 163, in constant
tensor_util.make_tensor_proto(value, dtype=dtype, shape=shape))
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/framework/tensor_util.py", line 421, in make_tensor_proto
tensor_proto.string_val.extend([compat.as_bytes(x) for x in proto_values])
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/util/compat.py", line 45, in as_bytes
(bytes_or_text,))
TypeError: Expected binary or unicode string, got <function length at 0x7f51a7a3ede8>
Edit:
Changing the tf.one_hot(lenght(output),max_length) gives me this error message:
Traceback (most recent call last):
File "tensorflow_test.py", line 184, in <module>
cross_entropy = cost(output,target)# How far am I from correct value?
File "tensorflow_test.py", line 121, in cost
cross_entropy = target * tf.log(output)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/ops/math_ops.py", line 754, in binary_op_wrapper
return func(x, y, name=name)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/ops/math_ops.py", line 903, in _mul_dispatch
return gen_math_ops.mul(x, y, name=name)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/ops/gen_math_ops.py", line 1427, in mul
result = _op_def_lib.apply_op("Mul", x=x, y=y, name=name)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/framework/op_def_library.py", line 703, in apply_op
op_def=op_def)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/framework/ops.py", line 2312, in create_op
set_shapes_for_outputs(ret)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/framework/ops.py", line 1704, in set_shapes_for_outputs
shapes = shape_func(op)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/ops/math_ops.py", line 1801, in _BroadcastShape
% (shape_x, shape_y))
ValueError: Incompatible shapes for broadcasting: (?, 14) and (?, 138915, 24)
tf.one_hot(length, ...)
here length is a function, not a tensor. Try length(something) instead.

tensorflow.python.framework.errors.OutOfRangeError:

Hi I am trying to run a conv. neural network addapted from MINST2 tutorial in tensorflow.
I am having the following error, but i am not sure what is going on:
W tensorflow/core/framework/op_kernel.cc:909] Invalid argument: Shape mismatch in tuple component 0. Expected [784], got [6272]
W tensorflow/core/framework/op_kernel.cc:909] Invalid argument: Shape mismatch in tuple component 0. Expected [784], got [6272]
Traceback (most recent call last):
File "4_Treino_Rede_Neural.py", line 161, in <module>
train_accuracy = accuracy.eval(feed_dict={keep_prob: 1.0})
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/framework/ops.py", line 555, in eval
return _eval_using_default_session(self, feed_dict, self.graph, session)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/framework/ops.py", line 3498, in _eval_using_default_session
return session.run(tensors, feed_dict)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/client/session.py", line 372, in run
run_metadata_ptr)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/client/session.py", line 636, in _run
feed_dict_string, options, run_metadata)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/client/session.py", line 708, in _do_run
target_list, options, run_metadata)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/client/session.py", line 728, in _do_call
raise type(e)(node_def, op, message)
tensorflow.python.framework.errors.OutOfRangeError: RandomShuffleQueue '_0_input/shuffle_batch/random_shuffle_queue' is closed and has insufficient elements (requested 100, current size 0)
[[Node: input/shuffle_batch = QueueDequeueMany[_class=["loc:#input/shuffle_batch/random_shuffle_queue"], component_types=[DT_FLOAT, DT_INT32], timeout_ms=-1, _device="/job:localhost/replica:0/task:0/cpu:0"](input/shuffle_batch/random_shuffle_queue, input/shuffle_batch/n)]]
Caused by op u'input/shuffle_batch', defined at:
File "4_Treino_Rede_Neural.py", line 113, in <module>
x, y_ = inputs(train=True, batch_size=FLAGS.batch_size, num_epochs=FLAGS.num_epochs)
File "4_Treino_Rede_Neural.py", line 93, in inputs
min_after_dequeue=1000)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/training/input.py", line 779, in shuffle_batch
dequeued = queue.dequeue_many(batch_size, name=name)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/ops/data_flow_ops.py", line 400, in dequeue_many
self._queue_ref, n=n, component_types=self._dtypes, name=name)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/ops/gen_data_flow_ops.py", line 465, in _queue_dequeue_many
timeout_ms=timeout_ms, name=name)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/ops/op_def_library.py", line 704, in apply_op
op_def=op_def)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/framework/ops.py", line 2260, in create_op
original_op=self._default_original_op, op_def=op_def)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/framework/ops.py", line 1230, in __init__
self._traceback = _extract_stack()
My program is:
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os.path
import time
import numpy as np
import tensorflow as tf
# Basic model parameters as external flags.
flags = tf.app.flags
FLAGS = flags.FLAGS
flags.DEFINE_integer('num_epochs', 2, 'Number of epochs to run trainer.')
flags.DEFINE_integer('batch_size', 100, 'Batch size.')
flags.DEFINE_string('train_dir', '/root/data', 'Directory with the training data.')
#flags.DEFINE_string('train_dir', '/root/data2', 'Directory with the training data.')
# Constants used for dealing with the files, matches convert_to_records.
TRAIN_FILE = 'train.tfrecords'
VALIDATION_FILE = 'validation.tfrecords'
# Set-up dos pacotes
sess = tf.InteractiveSession()
def read_and_decode(filename_queue):
reader = tf.TFRecordReader()
_, serialized_example = reader.read(filename_queue)
features = tf.parse_single_example(
serialized_example,
# Defaults are not specified since both keys are required.
features={
'image_raw': tf.FixedLenFeature([], tf.string),
'label': tf.FixedLenFeature([], tf.int64),
})
# Convert from a scalar string tensor (whose single string has
# length mnist.IMAGE_PIXELS) to a uint8 tensor with shape
# [mnist.IMAGE_PIXELS].
image = tf.decode_raw(features['image_raw'], tf.uint8)
image.set_shape([784])
# OPTIONAL: Could reshape into a 28x28 image and apply distortions
# here. Since we are not applying any distortions in this
# example, and the next step expects the image to be flattened
# into a vector, we don't bother.
# Convert from [0, 255] -> [-0.5, 0.5] floats.
image = tf.cast(image, tf.float32) * (1. / 255) - 0.5
# Convert label from a scalar uint8 tensor to an int32 scalar.
label = tf.cast(features['label'], tf.int32)
return image, label
def inputs(train, batch_size, num_epochs):
"""Reads input data num_epochs times.
Args:
train: Selects between the training (True) and validation (False) data.
batch_size: Number of examples per returned batch.
num_epochs: Number of times to read the input data, or 0/None to
train forever.
Returns:
A tuple (images, labels), where:
* images is a float tensor with shape [batch_size, 30,26,1]
in the range [-0.5, 0.5].
* labels is an int32 tensor with shape [batch_size] with the true label,
a number in the range [0, char letras).
Note that an tf.train.QueueRunner is added to the graph, which
must be run using e.g. tf.train.start_queue_runners().
"""
if not num_epochs: num_epochs = None
filename = os.path.join(FLAGS.train_dir,
TRAIN_FILE if train else VALIDATION_FILE)
with tf.name_scope('input'):
filename_queue = tf.train.string_input_producer(
[filename], num_epochs=num_epochs)
# Even when reading in multiple threads, share the filename
# queue.
image, label = read_and_decode(filename_queue)
# Shuffle the examples and collect them into batch_size batches.
# (Internally uses a RandomShuffleQueue.)
# We run this in two threads to avoid being a bottleneck.
images, sparse_labels = tf.train.shuffle_batch(
[image, label], batch_size=batch_size, num_threads=2,
capacity=1000 + 3 * batch_size,
# Ensures a minimum amount of shuffling of examples.
min_after_dequeue=1000)
return images, sparse_labels
def weight_variable(shape):
initial = tf.truncated_normal(shape, stddev=0.1)
return tf.Variable(initial)
def bias_variable(shape):
initial = tf.constant(0.1, shape=shape)
return tf.Variable(initial)
def conv2d(x, W):
return tf.nn.conv2d(x, W, strides=[1, 1, 1, 1], padding='SAME')
def max_pool_2x2(x):
return tf.nn.max_pool(x, ksize=[1, 2, 2, 1],
strides=[1, 2, 2, 1], padding='SAME')
#Variaveis
x, y_ = inputs(train=True, batch_size=FLAGS.batch_size, num_epochs=FLAGS.num_epochs)
#onehot_y_ = tf.one_hot(y_, 36, dtype=tf.float32)
#y_ = tf.string_to_number(y_, out_type=tf.int32)
#Layer 1
W_conv1 = weight_variable([5, 5, 1, 32])
b_conv1 = bias_variable([32])
x_image = tf.reshape(x, [-1,28,28,1])
h_conv1 = tf.nn.relu(conv2d(x_image, W_conv1) + b_conv1)
h_pool1 = max_pool_2x2(h_conv1)
#Layer 2
W_conv2 = weight_variable([5, 5, 32, 64])
b_conv2 = bias_variable([64])
h_conv2 = tf.nn.relu(conv2d(h_pool1, W_conv2) + b_conv2)
h_pool2 = max_pool_2x2(h_conv2)
#Densely Connected Layer
W_fc1 = weight_variable([7 * 7 * 64, 1024])
b_fc1 = bias_variable([1024])
h_pool2_flat = tf.reshape(h_pool2, [-1, 7*7*64])
h_fc1 = tf.nn.relu(tf.matmul(h_pool2_flat, W_fc1) + b_fc1)
#Dropout - reduz overfitting
keep_prob = tf.placeholder(tf.float32)
h_fc1_drop = tf.nn.dropout(h_fc1, keep_prob)
#Readout layer
W_fc2 = weight_variable([1024, 36])
b_fc2 = bias_variable([36])
#y_conv=tf.nn.softmax(tf.matmul(h_fc1_drop, W_fc2) + b_fc2)
y_conv = tf.matmul(h_fc1_drop, W_fc2) + b_fc2
#Train and evaluate
#cross_entropy = tf.reduce_mean(-tf.reduce_sum(y_ * tf.log(y_conv), reduction_indices=[1]))
#cross_entropy = tf.reduce_mean(-tf.reduce_sum(onehot_y_ * tf.log(y_conv), reduction_indices=[1]))
cross_entropy = tf.reduce_mean(tf.nn.sparse_softmax_cross_entropy_with_logits(y_conv, y_))
train_step = tf.train.AdamOptimizer(1e-4).minimize(cross_entropy)
correct_prediction = tf.equal(tf.argmax(y_conv,1), tf.argmax(y_,1))
accuracy = tf.reduce_mean(tf.cast(correct_prediction, tf.float32))
sess.run(tf.initialize_all_variables())
coord = tf.train.Coordinator()
threads = tf.train.start_queue_runners(sess=sess, coord=coord)
for i in range(20000):
if i%100 == 0:
train_accuracy = accuracy.eval(feed_dict={keep_prob: 1.0})
print("step %d, training accuracy %g"%(i, train_accuracy))
train_step.run(feed_dict={keep_prob: 0.5})
x, y_ = inputs(train=True, batch_size=2000)
#y_ = tf.string_to_number(y_, out_type=tf.int32)
print("test accuracy %g"%accuracy.eval(feed_dict={keep_prob: 1.0}))
coord.join(threads)
sess.close()
Can anyone explain me whats going on? And how to fix it?
Thanks!
Marcelo V
I had similar problems in the past, and it was due to that I was storing and reading the data in incorrect data types. For example, I had casted the data first as type float when converting original png data to tfrecords. Then when I read the data out from tfrecords, I once again casted it as float (assuming the data coming out was uint8. Hence I had mismatch of 3136 (784*4) when expected 784. I'm guessing that may also be the case for you here.
In the line:
filename_queue = tf.train.string_input_producer([filename], num_epochs=num_epochs)
You specify the number of epochs the queue will run through the filenames. The documentation explains it well:
num_epochs: An integer (optional). If specified, string_input_producer produces each string from num_epochs times before generating an OutOfRange error. If not specified, string_input_producer can cycle through the strings in string_tensor an unlimited number of times.
In flags.DEFINE_integer('num_epochs', 2, 'Number of epochs to run trainer.'), you specify a default number of epochs 2. You should either increase that, or remove the num_epochs argument in string_input_producer.

Variable scopes in Tensorflow

I am having problems making effective usage of variable scopes. I want to define some variables for weights, biases and inner state of a simple recurrent network. I call get_saver() once after defining the default graph. I then iterate over a batch of samples using tf.scan.
import tensorflow as tf
import math
import numpy as np
INPUTS = 10
HIDDEN_1 = 2
BATCH_SIZE = 3
def batch_vm2(m, x):
[input_size, output_size] = m.get_shape().as_list()
input_shape = tf.shape(x)
batch_rank = input_shape.get_shape()[0].value - 1
batch_shape = input_shape[:batch_rank]
output_shape = tf.concat(0, [batch_shape, [output_size]])
x = tf.reshape(x, [-1, input_size])
y = tf.matmul(x, m)
y = tf.reshape(y, output_shape)
return y
def get_saver():
with tf.variable_scope('h1') as scope:
weights = tf.get_variable('W', shape=[INPUTS, HIDDEN_1], initializer=tf.truncated_normal_initializer(stddev=1.0 / math.sqrt(float(INPUTS))))
biases = tf.get_variable('bias', shape=[HIDDEN_1], initializer=tf.constant_initializer(0.0))
state = tf.get_variable('state', shape=[HIDDEN_1], initializer=tf.constant_initializer(0.0), trainable=False)
saver = tf.train.Saver([weights, biases, state])
return saver
def load(sess, saver, checkpoint_dir = None):
print("loading a session")
ckpt = tf.train.get_checkpoint_state(checkpoint_dir)
if ckpt and ckpt.model_checkpoint_path:
saver.restore(sess, ckpt.model_checkpoint_path)
else:
raise Exception("no checkpoint found")
return
def iterate_state(prev_state_tuple, input):
with tf.variable_scope('h1') as scope:
scope.reuse_variables()
weights = tf.get_variable('W', shape=[INPUTS, HIDDEN_1], initializer=tf.truncated_normal_initializer(stddev=1.0 / math.sqrt(float(INPUTS))))
biases = tf.get_variable('bias', shape=[HIDDEN_1], initializer=tf.constant_initializer(0.0))
state = tf.get_variable('state', shape=[HIDDEN_1], initializer=tf.constant_initializer(0.0), trainable=False)
print("input: ",input.get_shape())
matmuladd = batch_vm2(weights, input) + biases
matmulpri = tf.Print(matmuladd,[matmuladd], message=" malmul -> ")
#matmulvec = tf.reshape(matmuladd, [HIDDEN_1])
#state = tf.get_variable('state', shape=[HIDDEN_1], initializer=tf.constant_initializer(0.0))
print("prev state: ",prev_state_tuple.get_shape())
unpacked_state, unpacked_out = tf.split(0,2,prev_state_tuple)
prev_state = unpacked_state
state = state.assign( 4.2*(0.9* prev_state + 0.1*matmuladd) )
#output = tf.nn.relu(state)
output = tf.nn.tanh(state)
state = tf.Print(state, [state], message=" state -> ")
output = tf.Print(output, [output], message=" output -> ")
#output = matmulpri
print(" state: ", state.get_shape())
print(" output: ", output.get_shape())
concat_result = tf.concat(0,[state, output])
print (" concat return: ", concat_result.get_shape())
return concat_result
def data_iter():
while True:
idxs = np.random.rand(BATCH_SIZE, INPUTS)
yield idxs
with tf.Graph().as_default():
inputs = tf.placeholder(tf.float32, shape=(BATCH_SIZE, INPUTS))
saver = get_saver()
initial_state = tf.zeros([HIDDEN_1],
name='initial_state')
initial_out = tf.zeros([HIDDEN_1],
name='initial_out')
#concat_tensor = tf.concat(0,[initial_state, initial_out])
concat_tensor = tf.concat(0,[initial_state, initial_out])
print(" init state: ",initial_state.get_shape())
print(" init out: ",initial_out.get_shape())
print(" concat: ",concat_tensor.get_shape())
scanout = tf.scan(iterate_state, inputs, initializer=concat_tensor, name='state_scan')
print ("scanout shape: ", scanout.get_shape())
state, output = tf.split(1,2,scanout, name='split_scan_output')
print(" end state: ",state.get_shape())
print(" end out: ",output.get_shape())
#output,state,diagnostic = create_graph(inputs, state, prev_state)
sess = tf.Session()
# Run the Op to initialize the variables.
sess.run(tf.initialize_all_variables())
if False:
load(sess, saver)
iter_ = data_iter()
for i in xrange(0, 5):
print ("iteration: ",i)
input_data = iter_.next()
out,st,so = sess.run([output,state,scanout], feed_dict={ inputs: input_data})
saver.save(sess, 'my-model', global_step=1+i)
print("input vec: ", input_data)
print("state vec: ", st)
print("output vec: ", out)
print(" end state (runtime): ",st.shape)
print(" end out (runtime): ",out.shape)
print(" end scanout (runtime): ",so.shape)
My hope would be to have the variables retrieved from get_variable inside the scan op to be the same as defined inside the get_saver call. However if I run this sample code I get the following output with errors:
(' init state: ', TensorShape([Dimension(2)]))
(' init out: ', TensorShape([Dimension(2)]))
(' concat: ', TensorShape([Dimension(4)]))
Traceback (most recent call last):
File "cycles_in_graphs_with_scan.py", line 88, in <module>
scanout = tf.scan(iterate_state, inputs, initializer=concat_tensor, name='state_scan')
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/ops/functional_ops.py", line 345, in scan
back_prop=back_prop, swap_memory=swap_memory)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/ops/control_flow_ops.py", line 1873, in while_loop
result = context.BuildLoop(cond, body, loop_vars)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/ops/control_flow_ops.py", line 1749, in BuildLoop
body_result = body(*vars_for_body_with_tensor_arrays)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/ops/functional_ops.py", line 339, in compute
a = fn(a, elems_ta.read(i))
File "cycles_in_graphs_with_scan.py", line 47, in iterate_state
weights = tf.get_variable('W', shape=[INPUTS, HIDDEN_1], initializer=tf.truncated_normal_initializer(stddev=1.0 / math.sqrt(float(INPUTS))))
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/ops/variable_scope.py", line 732, in get_variable
partitioner=partitioner, validate_shape=validate_shape)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/ops/variable_scope.py", line 596, in get_variable
partitioner=partitioner, validate_shape=validate_shape)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/ops/variable_scope.py", line 161, in get_variable
caching_device=caching_device, validate_shape=validate_shape)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/ops/variable_scope.py", line 454, in _get_single_variable
" Did you mean to set reuse=None in VarScope?" % name)
ValueError: Variable state_scan/h1/W does not exist, disallowed. Did you mean to set reuse=None in VarScope?
any idea what I am doing wrong in this example?
if False:
load(sess, saver)
This two lines lead to uninitialized variables.

python - Error with Mariana/Theano neural network

I am facing a problem when I start my trainer and I can't figure out the cause.
My input data is of dimension 42 and my output should be one value out of 4.
This is the shape of my training and test set:
Training set:
input = (1152, 42) target = (1152,)
Training set: input = (1152, 42) target = (1152,)
Test set: input = (384, 42) target = (384,)
This is the construction of my network:
ls = MS.GradientDescent(lr=0.01)
cost = MC.CrossEntropy()
i = ML.Input(42, name='inp')
h = ML.Hidden(23, activation=MA.Sigmoid(), initializations=[MI.GlorotTanhInit()], name="hid")
o = ML.SoftmaxClassifier(4, learningScenario=ls, costObject=cost, name="out")
mlp = i > h > o
And this is the construction of the datasets, trainers and recorders:
trainData = MDM.RandomSeries(distances = train_set[0], next_state = train_set[1])
trainMaps = MDM.DatasetMapper()
trainMaps.mapInput(i, trainData.distances)
trainMaps.mapOutput(o, trainData.next_state)
testData = MDM.RandomSeries(distances = test_set[0], next_state = test_set[1])
testMaps = MDM.DatasetMapper()
testMaps.mapInput(i, testData.distances)
testMaps.mapOutput(o, testData.next_state)
earlyStop = MSTOP.GeometricEarlyStopping(testMaps, patience=100, patienceIncreaseFactor=1.1, significantImprovement=0.00001, outputFunction="score", outputLayer=o)
epochWall = MSTOP.EpochWall(1000)
trainer = MT.DefaultTrainer(
trainMaps=trainMaps,
testMaps=testMaps,
validationMaps=None,
stopCriteria=[earlyStop, epochWall],
testFunctionName="testAndAccuracy",
trainMiniBatchSize=MT.DefaultTrainer.ALL_SET,
saveIfMurdered=False
)
recorder = MREC.GGPlot2("MLP", whenToSave = [MREC.SaveMin("test", o.name, "score")], printRate=1, writeRate=1)
trainer.start("MLP", mlp, recorder = recorder)
But the following error is being produced:
Traceback (most recent call last):
File "nn-mariana.py", line 82, in <module>
trainer.start("MLP", mlp, recorder = recorder)
File "SUPRESSED/Mariana/Mariana/training/trainers.py", line 226, in start
Trainer_ABC.start( self, runName, model, recorder, trainingOrder, moreHyperParameters )
File "SUPRESSED/Mariana/Mariana/training/trainers.py", line 110, in start
return self.run(runName, model, recorder, *args, **kwargs)
File "SUPRESSED/Mariana/Mariana/training/trainers.py", line 410, in run
outputLayers
File "SUPRESSED/Mariana/Mariana/training/trainers.py", line 269, in _trainTest
res = modelFct(output, **kwargs)
File "SUPRESSED/Mariana/Mariana/network.py", line 47, in __call__
return self.callTheanoFct(outputLayer, **kwargs)
File "SUPRESSED/Mariana/Mariana/network.py", line 44, in callTheanoFct
return self.outputFcts[ol](**kwargs)
File "SUPRESSED/Mariana/Mariana/wrappers.py", line 110, in __call__
return self.run(**kwargs)
File "SUPRESSED/Mariana/Mariana/wrappers.py", line 102, in run
fres = iter(self.theano_fct(*self.fctInputs.values()))
File "SUPRESSED/Theano/theano/compile/function_module.py", line 871, in __call__
storage_map=getattr(self.fn, 'storage_map', None))
File "SUPRESSED/Theano/theano/gof/link.py", line 314, in raise_with_op
reraise(exc_type, exc_value, exc_trace)
File "SUPRESSED/Theano/theano/compile/function_module.py", line 859, in __call__
outputs = self.fn()
ValueError: Input dimension mis-match. (input[0].shape[1] = 1152, input[1].shape[1] = 4)
Apply node that caused the error: Elemwise{Composite{((i0 * i1) + (i2 * log(i3)))}}[(0, 1)](InplaceDimShuffle{x,0}.0, LogSoftmax.0, Elemwise{sub,no_inplace}.0, Elemwise{sub,no_inplace}.0)
Toposort index: 18
Inputs types: [TensorType(int32, row), TensorType(float64, matrix), TensorType(int32, row), TensorType(float64, matrix)]
Inputs shapes: [(1, 1152), (1152, 4), (1, 1152), (1152, 4)]
Inputs strides: [(4608, 4), (32, 8), (4608, 4), (32, 8)]
Inputs values: ['not shown', 'not shown', 'not shown', 'not shown']
Outputs clients: [[Sum{axis=[1], acc_dtype=float64}(Elemwise{Composite{((i0 * i1) + (i2 * log(i3)))}}[(0, 1)].0)]]
Versions:
Mariana (1.0.1rc1, /media/guilhermevrs/Data/Documentos/Academico/TCC-code/Mariana)
Theano (0.8.0.dev0, SUPRESSED/Theano)
This code was produced having as base the tutorial code from the mnist example.
Could you please help me to figure out what's going on?
Thank you in advance
I talked directly to the authors of Mariana and the cause and solution is explained in this issue